Due to the way the integration with QuickBooks Online works, taxes aren't passed directly from Flex to QBO. Instead, Flex passes a code that tells QBO which tax rate to apply.
The way this works is vai name matching. In QBO, Taxes > Add/edit tax rates and agencies, take a look at the "Tax Name" entries. Those must match a "Rule Name" in Flex's System Settings > Sales Tax Rules entries. If there isn't a match, QBO will not calculate taxes.
Additionally, even if there is a match, QBO is going to use its settings for the tax rate, not those found in Flex. You must verify that the rates are the same in both applications.